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of 48 Hall, S.J.G. Effective population sizes in livestock estimated from census and herdbook data

Supplementary Table S1: Summary of Supplementary Tables

Key to table

Species data are in Tables S2-S6. Data on UK cattle relevant to calculation of Hill’s equation are in Supplementary Table S7. In Supplementary Table S8

further data are given on the ratio 𝑵𝒆/𝑵𝒄.

For Tables S” to S6, each table is in three parts: (a) relates to calculation of 𝑵𝒆(𝐷𝐹), (b) to 𝑵𝒆(𝐿𝐷) and (c) to literature references.

Column headings for parts (a) and (b) are as follows:

Breed: name of breed

Country: Location of animals studied

Source: authority for census data. DAD-IS signifies data are from the FAO database http://dad.fao.org/ accessed during December 2015 and January 2016

Year: year to which census data relate

brdg M, brdg F: numbers of breeding males and females according to the cited source

hbk F: number of registered, currently breeding females, when given by the cited source

“total”: statement of total numbers, when given by the cited source

Ne by DF (in part (a)): 𝑵𝒆(𝐷𝐹)

Ref DF (in part (a)): literature citation (listed in part (c))

Ne by LD (in part (b)): 𝑵𝒆(𝐿𝐷)

Ref LD (in part (b)): literature citation (listed in part (c))

Reference year: period to which the calculated 𝑵𝒆(𝐷𝐹) or 𝑵𝒆(𝐿𝐷) applies

Adopted total: 𝑵𝑐 used in current study

http://dad.fao.org/


Supplementary Table S2: Cattle

Key to table: see Supplementary Table S1

Part (a) Breeds with 𝑵𝒆(𝐷𝐹)

Breed country source year brdg M

brdg F hbk F "total" Ne by DF

Ref DF Reference year

Adopted total

Aberdeen Angus Brazil (18) (71) 2013 26985 239.5 (19) 2008-2010 26985

Abondance France DAD-IS 2001 800 55000 15500 43.5 (36) 2002-2007 55000

Afrikaner S Africa DAD-IS 2011 6764 167.5 (50) 2015 6764

Alentejana Portugal DAD-IS 2010 291 25890 46922 23.3 (38) 2000-2003 46922

Alistana-Sanabresa

Spain (2) 1995 279 36 (2) 1996 279

Asturiana de las Montanas

Spain (2) 1995 4629 35 (2) 1996 4629

Asturiana de los Valles

Spain (2) 1995 7863 89 (2) 1996 7863

Aubrac France DAD-IS 2001 1560 92000 33000 285.3 (36) 2002-2007 92000

Avilena-Negra Iberica

Spain (2) 1995 2535 40 (2) 1996 2535

Ayrshire Canada (11) 2006 255 11636 54 (17) 2003-2007 11636

Ayrshire S Africa DAD-IS 1998 270 8775 148 (12) 2002 8775

Ayrshire USA DAD-IS 2000 6046 161 (30) (32) 2001 6046

Ayrshire UK (72) (73) 2011 405 3053 11264 94 (72) 2007 11264

Bazadaise France DAD-IS 2001 54 2800 2500 100.3 (36) 2002-2007 2800

Blonde d'Aquitaine

France DAD-IS 2001 11988 400000 32000 142 (36) 2002-2007 400000

Brangus S Africa (8) 2008 18000 166.7 (8) 2008 18000

Brangus Argentina (74) 2004 210 5415 5625 274 (74) 2004 5625

Braunvieh Austria DAD-IS 1994 1000 69092 109 (27) 1993 69092

Braunvieh Switzerland DAD-IS 2002 1175 300892 425000 113.8 (49) 2005 425000

British White UK (72) (73) 2011 100 398 1485 36 (72) 2007 1485

Brown Swiss Canada (11) 2006 193 3224 47 (17) 2003-2007 3224

Brown Swiss USA DAD-IS 2000 10648 61 (30) (32) 2001 10648

Brown-Swiss France DAD-IS 2001 29 31000 12000 79.5 (36) 2002-2007 31000

Bruna dels Pireneus

Spain (2) 1995 2809 95 (2) 1996 2809

Canadienne Canada (11) 2006 408 40 (17) 2003-2007 408





Adopted total

Carinthian Blond Austria DAD-IS 2001 30 566 566 2200 76 (3) 1997-2002 566

Charolais Denmark (22) 2015 6500 558 (16) 2009 6500

Charolais Ireland DAD-IS 2006 8055 22268 22268 244 (16) 2009 22268

Charolais France (10) 2014 1575986 493 (16) 2008 1575896

Charolais France DAD-IS 2001 52500 1600000 105000 500.5 (36) 2002-2007 1600000

Chianina Italy DAD-IS 2002 463 13971 13971 138 (31) 2000 13971

Criollo Argentina (4) 25 (4) 1993-1997

Dairy Shorthorn UK (72) (73) 2011 9009 500 (72) 2007 9009

Dairy Swiss (Brown Swiss)

S Africa (7) 2013 1135 1135 89 (7) 2008 1135

Danish Red Denmark DAD-IS 1997 100 96000 59000 47 (32) 2000-2005 96000

Devon Brazil (18) (71) 2009 5883 110 (19) 2008-2010 5883

Eringer Switzerland DAD-IS 2009 286 8000 8350 321 (37) 2009 8350

Ferrandaisex France DAD-IS 2001 34 600 506 54.5 (36) 2002-2007 600

Flamandex France DAD-IS 2001 40 140 140 63.5 (36) 2002-2007 140

French Red Pied France DAD-IS 2001 15 25000 4000 170 (36) 2002-2007 25000

French Simmental

France DAD-IS 2001 60 35000 6000 140 (36) 2002-2007 35000

Gasconne France DAD-IS 2001 950 25000 11000 256.3 (36) 2002-2007 25000

German Holstein Germany DAD-IS 1998 7583 1514413 1521996 52 (39) 1996-1999 1521996

German Red Germany DAD-IS 2008 69 918 987 47 (48) 2008 987

Gir Brazil (1) 2009 130 (13) 2002-2010 3000000

Gir Brazil DAD-IS 1992 2250 90000 130000 45 (29) 1998 130000

Girolando Brazil (23) 2000 200000 188 (23) 2008 200000

Grauvieh Austria DAD-IS 1993 40 3389 73 (27) 1993 3389

Guernsey Canada (11) 2006 43 438 46 (17) 2003-2007 438

Guernsey USA DAD-IS 2000 6151 65 (30) (32) 2001 6151

Guernsey S Africa DAD-IS 1998 52 1863 165 (12) 2002 1863

Guernsey UK (72) (73) 2011 99 971 4116 105 (72) 2007 4116

Guzerat Brazil (6) 2008 92000 98 (14) 2008 92000

Guzerat Brazil DAD-IS 1992 1500 54600 84000 101 (29) 1998 84000

Hanwoo Korea DAD-IS 2003 84 (40) 2006-2008 1239380

Hereford Brazil (18) (71) 2009 8064 157 (19) 2008-2010 8064

Hereford Ireland DAD-IS 2006 350 3500 64 (33) 2000-2005 3500

Hereford USA DAD-IS 2001 98444 85 (32) 2000-2005 98444





Adopted total

Highland UK (72) (73) 2009 358 1793 6081 118 (72) 2007 6081

Hinterwald Germany DAD-IS 2013 98 521 521 127.2 (41) 2011 521

Holstein USA DAD-IS 2000 317567 39 (30) (32) 2001 317567

Holstein Denmark DAD-IS 1997 3000 542000 396000 600000 49 (32) 2000-2005 600000

Holstein Ireland DAD-IS 2006 2246 257342 257342 75 (33) 2000-2005 257342

Holstein S Africa DAD-IS 1998 2092 132113 132113 137 (12) 2002 132113

Holstein France DAD-IS 2001 3100000 1889000 74.3 (36) 2002-2007 3100000

Icelandic Iceland DAD-IS 2004 78 30353 64639 125 (34) 2003-2005 64639

Indubrasil Brazil DAD-IS 1991 80000 200000 41 (15) 1998 200000

Japanese Black Japan (26) 1999 530000 17 (26) 2001 530000

Jersey USA DAD-IS 2000 67776 30 (30) (32) 2001 67776

Jersey Denmark DAD-IS 1997 100000 74500 53 (32) 2000-2005 100000

Jersey S Africa 108 (12) 2002

Lidia Spain DAD-IS 2008 5448 115068 269582 35.7 (42) 2004-2012 269582

Lidia (Domecq) Spain 26.9 (28) 2006

Limousin Denmark (25) 2015 1667 (16) 2009 20000

Limousin Ireland DAD-IS 2006 6021 18011 345 (16) 2009 18011

Limousin France DAD-IS 2001 16000 825000 50000 376.3 (36) 2002-2007 825000

Limousin France (16) 2008 2459 (16) 2008

Limpurg Germany DAD-IS 2013 26 135 135 39.3 (41) 2011 135

Lincoln Red UK (72) (73) 2011 155 810 2499 82 (72) 2499

Longhorn UK (72) (73) 2009 309 1613 5766 82 (72) 5766

Luing UK (72) (73) 2011 227 1894 7194 112 (72) 7194

Maine-Anjou France DAD-IS 2001 1600 85000 8000 211.5 (36) 2002-2007 85000

Marchigiana Italy DAD-IS 2002 320 19350 41930 122 (31) 2000 41930

Maremmana Italy DAD-IS 2002 103 3116 3116 111 (32) 2000-2005 3116

Mertolenga Portugal DAD-IS 2013 217 31209 56415 25 (32) 2000-2005 56415

Milking Shorthorn Canada (11) 2006 390 66 (17) 2003-2007 390

Montbéliarde France DAD-IS 2001 435 692000 168341 56.8 (36) 2002-2007 168341

Morucha Spain (2) 1995 1547 27 (2) 1996 1547

Mucca Pisana Italy DAD-IS 2002 8 154 20 (32) 2000-2005 154

Nelore Brazil DAD-IS 1991 2500000 68 (29) 1998 2500000

Nguni S Africa (24) 2006 697 11611 12308 168 (24) 2012 12308

Normande France DAD-IS 2001 14 810000 190000 64.3 (36) 2002-2007 810000

Norwegian Red Norway DAD-IS 2011 130 195000 200000 173 (43) 2007-2009 200000





Adopted total

Original Braunvieh

Switzerland DAD-IS 2000 500 9000 10250 73 (49) 2005 10250

Original Pinzgau Austria (3) (70) 9706 76 (3) 1997-2002 9706

Original Swiss Brown


Pajuna Spain (5) 797 17 (5) 2011 797

Parthenaise France DAD-IS 2001 533 15000 7000 212 (36) 2002-2007 15000

Pinzgauer Austria (27) 1998 12232 53875 232 (27) 1993 53875

Pinzgauer Austrian beef

Austria (20) 2012 3143 107 (20) 2012 3143

Pinzgauer Austrian dairy

Austria (20) 2012 7479 122 (20) 2012 7479

Pinzgauer Slovak beef

Slovakia (20) 2012 637 809 (20) 2012 637

Pinzgauer Slovak dairy

Slovakia (20) 2012 1183 189 (20) 2012 1183

Pirenaica Spain (2) 1995 13117 123 (2) 1996 13117

Polled Nelore Brazil 1991 10000 17500 124 (15) 1998 17500

Red Angus USA DAD-IS 2000 51413 445 (35) 2005 51413

Red Poll UK (72) (73) 2011 159 868 3242 65 (72) 2007 3242

Romagnola Italy DAD-IS 2006 3480 13294 13294 124 (31) 2000 13294

Salers France DAD-IS 2000 5000 185000 28000 148 (36) 2002-2007 185000

Sayaguesa Spain (2) 1995 114 21 (2) 1996 114

Shorthorn Brazil (18) (71) 2009 336 210.5 (19) 2008-2010 336

Simmental Ireland DAD-IS 2006 1689 5970 127 (33) 2000-2005 5970

Simmental Austria DAD-IS 1998 1519 230181 258 (27) 1993 230181

Sindi Brazil (9) 2006 669 9 (15) 1998 669

Slovak Holstein Slovakia DAD-IS 2013 54623 162085 145.5 (45) 2011 54623

Slovak Pinzgauer Slovakia DAD-IS 2013 1430 12716 195 (45) 2011 12716

Slovak Spotted Slovakia DAD-IS 2013 29715 172361 434.5 (45) 2011 172361

South Devon UK (72) (73) 2011 527 3322 11750 97 (72) 2007 11750

Spanish Holstein Spain DAD-IS 2013 749 490486 744245 79.4 (46) 2012 744245

Tabapuã Brazil DAD-IS 1991 2200 4000 54 (15) 1998 4000

Tarentaise France DAD-IS 2001 140 14000 11300 53 (36) 2002-2007 14000

Tudanca Spain DAD-IS 2008 231 6967 10059 24 (47) 2011 10059





Adopted total

Tux-Zillertal Austria DAD-IS 2001 46 521 521 1000 43 (3) 1997-2002 1000

Tyrol Grey Austria DAD-IS 2013 34 3773 17728 102 (70) 2013 17728

Vorderwald Germany DAD-IS 2013 238 6439 6439 124.2 (41) 2011 6439

Vosgienne France DAD-IS 2001 56 4000 864 59.8 (36) 2002-2007 4000

Wagyu USA (21) (71) 2011 1386 17 (21) 2011 1386

Welsh Black UK (72) (73) 2010 345 2131 7884 500 (72) 2007 7884

Whitebred Shorthorn

UK (72) (73) 2011 28 90 154 97 (72) 2007 154


Part (b) Breeds with 𝑵𝒆(𝐿𝐷)


brdg F "total" "global" Ne by LD/SNP

Ref LD Reference year

Adopted total

Afrikaner S Africa DAD-IS 2011 6764 41 (52) 2013 6764

Anatolian Black

Turkey 183.7 (53) 1990-1999

Angus USA&NZ (1) 2009 10000000 136 (1) 2007-2009 10000000

Beefmaster USA (1) 2009 1000000 106 (1) 2007-2009 1000000

Belgian Blue Belgium DAD-IS 1994 3500 529129 1500000 68.36 (53) 1990-1999 1500000

Bonsmara S Africa DAD-IS 2011 50399 77 (52) 2013 50399

Brahman USA&Aus (1) 2009 4000000 115 (1) 2007-2009 4000000

Braunvieh Germany DAD-IS 1997 1172 176121 177293 84.45 (53) 1990-1999 177293

Brown Swiss USA (1) 2009 7000000 61 (1) 2007-2009 7000000

Canadian Angus

Canada (63) 2014 1500000 207 (65) 2010 1500000

Canadian Charolais

Canada (64) 2015 21498 285 (65) 2010 21498

Charolais USA (1) 2009 1200000 110 (1) 2007-2009 1200000

Chinese Holstein

China (57) 2011 11520000 45 (67) 2010 11520000

Chinese Simmental

China (60) 2010 30000 73 (68) 2011 30000

Cinisara Italy DAD-IS 2014 363 2825 4553 19 1999-2010 4553

Dairy Gir Brazil (61) 2002 58260 39 (69) 2008 58260

Danish Red Denmark (58) 2003 50000 74 (54) 2009 50000

Drakensberger S Africa DAD-IS 2011 6255 87 (52) 2013 6255

East African Shorthorned Zebu

100 (66) 2012

Eringer Switzerland DAD-IS 2009 286 8000 8350 118 (37) 2009 8350

Finnish Ayrshire

Finland DAD-IS 2009 182169 200000 73 (54) 2009 200000

Franken Gelbvieh

Germany DAD-IS 1997 38 8552 8590 109.95 (53) 1990-1999 8590

Galloway Germany DAD-IS 1997 1327 9513 10840 110.74 (53) 1990-1999 10840

German Fleckvieh

Germany DAD-IS 1997 2714 693422 696136 126.53 (53) 1990-1999 696136





Adopted total

Gir Brazil (1) 2009 3000000 133 (1) 2002-2010 3000000

Guernsey USA&UK (1) 2009 75000 76 (1) 2007-2009 75000

Hanwoo Korea DAD-IS 2003 1239380 84 (40) 2006-2008 1239380

Hereford USA&NZ (1) 2009 5000000 97 (1) 2007-2009 5000000

Holstein USA&NZ (1) 2009 65000000 99 (1) 2007-2009 65000000

Holstein Korea DAD-IS 2012 19 258754 420113 122 (55) 2011 420113

Illyrian Mountain Busa

Albania 149.76 (53) 1990-1999

Istrian Croatia (62) 2013 40 721 12.3 (62) 2012 721

Jersey USA&NZ (1) 2009 2500000 73 (1) 2007-2009 2500000

Kermani Iran n/a 23 (51) 2013

Kurdi Iran 1998 200000 29 (51) 2013 200000

Limousin USA&FR (1) 2009 4000000 174 (1) 2007-2009 4000000

Mazandarani Iran 107 (51) 2013

Modicana Italy DAD-IS 2006 298 3203 3501 12 1999-2010 3501

Murnau-Werdenfelser

Germany DAD-IS 1997 6 152 158 52.64 (53) 1990-1999 158

Najdi Iran (59) 2013 380000 22 (51) 2013 380000

N'Dama Guinea (1) 2009 7000000 228 (1) 2007-2009 7000000

Nelore Brazil (1) (71) 2009 755977 10000000 86 (1) 2007-2009 10000000

Nguni S Africa DAD-IS 2011 9462 95 (52) 2013 9462

Norwegian Red

Norway DAD-IS 2011 130 195000 200000 194 (56) 2007-2009 200000

Original Braunvieh

Switzerland DAD-IS 1997 10 157 167 92.31 (53) 1990-1999 167

Original Swiss Brown


Pars Iran 45 (51) 2013

Piedmontese Italy DAD-IS 2013 2327 124406 262935 400000 167 (1) 2007-2009 262935

Red Angus USA&Can (1) 2009 300000 85 (1) 2007-2009 300000

Red Holstein Germany DAD-IS 1997 2006 210523 212529 111.48 (53) 1990-1999 212259

Romagnola Italy DAD-IS 2007 3257 13237 16494 30000 92 (1) 2007-2009 16494





Adopted total

Santa Gertrudis

USA (1) 2009 5000000 107 (1) 2007-2009 5000000

Sarabi Iran (59) 750000 13 (51) 2013 750000

Sheko Ethiopia (1) 2009 5000 5000 145 (1) 2007-2009 5000

Sistani Iran n/a 17 (51) 2013

Spanish Holstein

Spain DAD-IS 2013 749 490486 744245 74.4 (46) 2012 744245

Swedish Red & White

Sweden DAD-IS 2011 113237 385298 84 (54) 2009 385298

Taleshi Iran DAD-IS 1997 1000-10000

22 (51) 2013 5000

Tyrol Grey Austria DAD-IS 2013 34 3773 17728 17728 80 (70) 2013 17728


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(47)Sainz,R., Garcia,J.A., De Arguello,S., Barquin,F., Crespo,M.J., Chomon,N., Calderon,L.A. & Canon,J. (2011) Genetic structure of the Tudanca bovine breed inferred from the genealogical information. Archivos de Zootecnia, 60, 401-404.

(48)Kehr,C., Klunker,M., Fischer,R., Groeneveld,E. & Bergfeld,U. (2010) Monitoring of genetic diversity in livestock: Results for the population Rotes Höhenvieh. Züchtungskunde, 82, 387-399.

(49)Hagger,C. (2005) Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information. Journal of Animal Breeding and Genetics, 122, 405-413.

(50)Pienaar,L., Neser,F.W.C., Grobler,D., Scholtz,M.M. & MacNeil,M.D. (2015) Pedigree analysis of the Afrikaner cattle breed. Animal Genetic Resources, 57, 51-56.

(51)Karimi,K., Koshkoiyeh,A.E., Fozi,M.A., Porto-Neto,L.R. & Gondro,C. (2015) Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data. Conservation Genetics.

(52)Makina,S.O., Taylor,J.F., van Marle-Koster,E., Muchadeyi,F.C., Makgahlela,M.L., MacNeil,M.D. & Maiwashe,A. (2015) Extent of linkage disequilibrium and effective population size in four S African Sanga cattle breeds. Frontiers in Genetics, 6.

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(54)Rius-Vilarassa, E., Vilkki, J., Stranden, I., Schulman, N., Iso-Touru, T., Guldbrandtsen, B., Strandberg, E., Lund, M. S., and Fikse, W. F. Characterization of linkage disequilibrium in a Danish, Swedish and Finnish Red Breed cattle population. Proc 11th EAAP, Stavanger, 31 August 2011 . 2011.

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(64)Canadian Charolais (2015) Canadian Charolais numbers. pers comm.

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(66)Mbole-Kariuki,M.N., Sonstegard,T.S., Orth,A., Thumbi,S.M., Bronsvoort,B.M.d.C., Kiara,H., Toye,P., Conradie,I., Jennings,A., Coetzer,K., Woolhouse,M.E.J., Hanotte,O. & Tapio,M. (2014) Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya. Heredity, 113, 297-305.

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Supplementary Table S3: Sheep references


Part (a) Breeds with 𝑵𝒆(𝛥𝐹)

Breed country source year brdg

M brdg F hbk F "total" Ne by DF Ref DF

Reference year

Adopted total

Avranchin France DAD-IS 2001 39 537 180 537 48 (6) 2007 537

Basco-bearnaise France DAD-IS 2001 1805 76000 21076 76000 48 (6) 2007 76000

Basco-bearnaise France (2) 2009

24000

24000 112 (2) 2009 24000

Berrichon France (1) 2000 2970 141000 3300 141000 120 (1) (23) 2007 141000

Berrichon de l'Indre France DAD-IS 1994 30 1500 180 1500 35 (6) 2007 1500

Berrichon du Cher France DAD-IS 2001 2970 141000 3300 141000 50 (6) 2007 141000

Bizet France DAD-IS 2001 76 7000 5336 7000 257 (6) 2007 7000

Black Welsh Mountain UK (28) (29) 2007

1159 135 (28) 2007 1159

Blanc du Massif Central France DAD-IS 2001 7840 400000 35684 400000 108 (6) 2007 400000

Bleu du Maine France DAD-IS 2001 970 3000 1703 3000 293 (6) 2007 3000

Bleu du Maine France (1) 2000 970 3000 1703 14300 231 (1) (23) 2007 14300

Border Leicester UK (28) (29) 2007

1082 100 (28) 2007 1082

Boreray UK (28) (29) 2011 31 109

204 25 (28) 2007 204

Boulonnais France DAD-IS 2001 80 3000 2313 3000 80 (6) 2007 3000

Cambridge UK (28) (29) 2007

302 44 (28) 2007 302

Castlemilk Moorit UK (28) (29) 2011 54 216

538 61 (28) 2007 538

Causse du lot France DAD-IS 2001 1170 150000 32281 150000 101 (6) 2007 150000

Charmoise France DAD-IS 2001 1176 20000 3800 20000 77 (6) 2007 20000

Charmoise France (1) 2000 1176 20000 3800 23900 182 (1) (23) 2007 23900




Reference year

Adopted total

Charollais France DAD-IS 2001 1576 374000 10000 374000 85 (6) 2007 374000

Clun Forest UK (28) (29) 2007

2971 156 (28) 2007 2971

Clun forest France DAD-IS 2001

300 75 300 85 (6) 2007 300

Corse France DAD-IS 2001 3360 90000 18303 90000 375 (6) 2007 90000

Cotentin France DAD-IS 2001 200 2000 224 2000 38 (6) 2007 2000

Cotentin France (1) 2000 200 2000 224 6000 108 (1) (23) 2007 6000

Cotswold UK (28) (29) 2007

914 61 (28) 2007 914

Devon Closewool UK (28) (29) 2007 85 3279

3364 152 (28) 2007 3364

Dorset France DAD-IS 2001 40 2000 142 2000 21 (6) 2007 2000

Dorset Down UK (28) (29) 2007 56 1327

811 227 (28) 2007 811

Est à laine merinos France DAD-IS 2001 960 50000 4386 50000 86 (6) 2007 50000

Finnish France DAD-IS 2001 100 255 255 255 96 (6) 2007 255

Finnsheep Finland DAD-IS 2011

43841

43841 120 (8) 2012 43841

Grivette France DAD-IS 2001 72 15000 7141 15000 112 (6) 2007 15000

Hampshire France DAD-IS 2001 80 4000 685 4000 68 (6) 2007 4000

Hampshire Down UK (28) (29) 2007

3139 86 (28) 2007 3139

Hebridean UK (28) (29) 2007 217 1586

4483 443 (28) 2007 4483

Herdwick UK (28) (29) 2007

8000 500 (28) 2007 8000

Ile de France France DAD-IS 2001 7920 260000 17355 260000 55 (6) 2007 260000

Kerry Hill UK (28) (29) 2007

3079 500 (28) 2007 3079

Kres (Creska ovca) Croatia (3) 2009

15000 123 (10) 2007 15000

Krk Island Croatia (3) 2009

15000 26 (10) 2007 15000

Lacaune dairy France DAD-IS 2001 6000 840000 165986 840000 66 (6) 2007 840000




Reference year

Adopted total

Lacaune Viande France DAD-IS 2001 3900 443500 36122 443500 73 (6) 2007 443500

Leicester Longwool UK (28) (29) 2011 41 200

470 47 (28) 2007 470

Limousin France (1) 2000 117 150000 17450 150000 360 (1) (23) 2007 150000

Lincoln Longwool UK (28) (29) 2011 72 278

991 122 (28) 2007 991

Manech tête noire France DAD-IS 2001 2925 122000 18216 122000 38 (6) 2007 122000

Manech tête noire France (2) 2009

13000

13000 89 (2) 2009 13000

Manech tête rousse France DAD-IS 2001 4512 214000 73597 214000 77 (6) 2007 214000

Manech tête rousse France (2) 2009

76000

76000 174 (2) 2009 76000

Manx Loaghtan UK (28) (29) 2011 79 335

869 38 (28) 2007 869

Merino de Grazalema Spain (9) 2011

4912 24 (9) 2011 4912

Merinos d'Arles France DAD-IS 2001 4450 250000 23000 250000 182 (6) 2007 250000

Milk Lacaune France (2) 2009

170000

170000 143 (2) 2009 170000

Navajo Churro USA DADIS 2010 46 314

314 92 (7) 2004 314

Noir du Velay France DAD-IS 2001 490 25000 13480 25000 192 (6) 2007 25000

Norfolk Horn UK (28) (29) 2011 94 390

1025 90 (28) 2007 1025

North Ronaldsay UK (28) (29) 2011 42 150

394 124 (28) 2007 394

Oxford Down UK (28) (29) 2011 100 410

1006 83 (28) 2007 1006

Portland UK (28) (29) 2011 45 373

802 96 (28) 2007 802

Prealpes France DAD-IS 2001 4750 263000 12258 263000 55 (6) 2007 263000

Rava France DAD-IS 2001 95 40000 10500 40000 76 (6) 2007 40000

Romane France DAD-IS 2001 475 44500 13000 44500 101 (6) 2007 44500

Romanov France DAD-IS 2001 136 5000 3866 5000 43 (6) 2007 5000




Reference year

Adopted total

Romanov France (1) 2000 136 5000 3866 9100 78 (1) (23) 2007 9100

Romanov-INRA France (1) 2000

132 65 (1) (23) 2007 132

Rouge de l'Ouest France DAD-IS 1994 5000 240000 10481 240000 85 (6) 2007 240000

Roussin de la Hague France DAD-IS 2001 300 3000 1212 3000 163 (6) 2007 3000

Roussin de la Hague France (1) 2000 300 3000 1212 21500 172 (1) (23) 2007 21500

Ryeland UK (28) (29) 2007

2866 93 (28) 2007 2866

Santa Ines Brazil DAD-IS 1992 525 35000

35000 76 (5) 2008 35000

Soay UK (28) (29) 2011 156 535

1142 30 (28) 2007 1142

Solognote France DAD-IS 2001 80 2500 474 2500 72 (6) 2007 2500

Solognote France (1) 2000 80 2500 474 3100 154 (1) (23) 2007 3100

Southdown France DAD-IS 2001 26 2000 678 2000 42 (6) 2007 2000

Suffolk UK (28) (29) 2007

22255 420 (28) 2007 22255

Suffolk France DAD-IS 2001 28500 38000 6618 38000 69 (6) 2007 38000

Swaledale UK (28) (29) 2007

162900 420 (28) 2007 162900

Tarasconnaise France DAD-IS 2001 2200 120000 15000 120000 55 (6) 2007 120000

Teeswater UK (28) (29) 2007

655 - (28) 2007 655

Texel France DAD-IS 2001 4800 17459 11454 17459 82 (6) 2007 17459

Vendéen France DAD-IS 2001 2475 225000 12150 225000 76 (6) 2007 225000

Wensleydale UK (28) (29) 2007

991 238 (28) 2007 991

Whitefaced Woodland UK (28) (29) 2007 43 216

494 98

494

Zandi Iran (4) 2005

450

450 66 (4) 2005 450




M brdg F "total"

Ne by

LD/SNP Ref LD

Reference year

Adopted total

African Dorper South Africa DAD-IS 1992 60000 3900000

264 (11) 2012 3900000

Afshari Iran (21)

465 (11) 2012 2400000

Altamurana Italy DAD-IS 2013 101 712

469 (11) 2012 712

Australian Industry Merino Australia

853 (11) 2012

Australian Merino Australia

833 (11) 2012

Australian Poll Dorset Australia

318 (11) 2012

Australian Poll Merino Australia

918 (11) 2012

Australian Suffolk Australia DAD-IS

569 (11) 2012 6295

Bangladeshi Bangladesh

582 (11) 2012

Bangladeshi Garole Bangladesh

437 (11) 2012

Barbados Black Belly USA

374 (11) 2012

Black Headed Mutton Germany DAD-IS 2013 357 8856 8856 247 (11) 2012 8856

Border Leicester Australia DAD-IS

140 (12) 2015 33142

Border Leicester UK DAD-IS 2012

1082 451 242 (11) 2012 1082

Brazilian Creole Brazil

371 (11) 2012

Bundner Oberlander Switzerland DAD-IS 2013 115 800 679 253 (11) 2012 800

Castellana Spain DAD-IS 2013 639 18661

546 (11) 2012 18661

Changthangi India DAD-IS 2003 21611 30754

684 (11) 2012 30754

Chinese Merino China DAD-IS 1983 200 30000

397 (11) 2012 30000

Chios Greece DAD-IS 2013 4140 78690 16789 334 (11) 2012 78690

Churra Portugal

600 (11) 2012

Comisana Italy DAD-IS 2013 2539 48104

589 (11) 2012 48104



M brdg F "total"

Ne by

LD/SNP Ref LD

Reference year

Adopted total

Comisano Italy DAD-IS 2013 2539 48104

400 (13) 2014 48104

Cyprus Fat Tail Cyprus DAD-IS 2006 28 700

203 (11) 2012 700

Dairy Lacaune France (27)

192 (15) 2014 900000

Deccani India

837 (11) 2012

Dorper Australia

67 (16) 2014

Dorset Horn Australia DAD-IS 2012

938 391 134 (11) 2012 938

East Friesian Brown Germany DAD-IS 2011 16 143 143 186 (11) 2012 143

Engadine Red Switzerland DAD-IS 2013 280 3000 2897 482 (11) 2012 3000

Ethiopian Menz Ethiopia DAD-IS 1992

1260 (11) 2012 1692070

Finnsheep Finland DAD-IS 2011

43841

795 (11) 2012 43841

Galway Ireland DAD-IS 2012 50 1050 1050 322 (11) 2012 1050

Garut India (19)

337 (11) 2012 509436

German Mutton Merino Germany

74 (16) 2014

German Texel Germany DAD-IS 2013 255 3214 3214 448 (11) 2012 3214

Gulf Coast Native USA (24)

2000

611 (11) 2012 2000

Indian Garole India (18)

364 (11) 2012 206720

Irish Suffolk Ireland DAD-IS 2012 550 10000 10000 300 (11) 2012 10000

Leccese Italy DAD-IS 2013 13 610

556 (11) 2012 610

Meat Lacaune France DAD-IS 2001 3900 443500 36122 835 (11) 2012 443500

Merino Australia (17) 2003

348 (12) 2014 85000000

Merinolandschaf Germany DAD-IS 2013 486 14617 14617 407 (11) 2012 14617

Milk Lacaune France DAD-IS 2001 6000 840000 165986 714 (11) 2012 840000



M brdg F "total"

Ne by

LD/SNP Ref LD

Reference year

Adopted total

Moghani Iran (20) 1999

5500000

825 (11) 2012 5500000

Morada Nova Brazil DAD-IS 1992 22500 405000

327 (11) 2012 405000

New Zealand Romney New Zealand na

405 (11) 2012

New Zealand Texel New Zealand na

282 (11) 2012

Norduz Turkey (22)

285 (11) 2012 200

Ojalada Spain DAD-IS 2013 192 9340 9340 588 (11) 2012 9340

Pinzirita Italy DAD-IS 2013 695 21839

685 (13) 2014 21839

Poll Dorset Australia

152 (12) 2015

Qezel (Red Karaman, Morkaraman) Turkey DAD-IS

1317 (11) 2012 8000000

Rambouillet France

709 (11) 2012

Rasa Aragonesa Spain DAD-IS 2013 13601 462613 462613 780 (11) 2012 462613

Red Maasai Tanzania DAD-IS 2008 4500 270000

1070 (11) 2012 270000

Sakiz Turkey DAD-IS 2013 100 1400 406 165 (11) 2012 1400

Santa Ines Brazil DAD-IS 1992 525 35000

520 (11) 2012 35000

Sardinian Ancestral Black (Sarda) Italy DAD-IS 2013 23236 466837

306 (11) 2012 466837

Scottish Blackface UK (26)

528 (11) 2012 2500000

Scottish Texel UK

305 (11) 2012

Soay UK DAD-IS 2012

1142 476 194 (11) 2012 1142

Spael White Norway DAD-IS 2013 1255 31200

339 (11) 2012 84561

Spanish Churra Spain DAD-IS 2013 2514 160016

128 (14) 2012 175359

Sumatran Indonesia

336 (11) 2012



M brdg F "total"

Ne by

LD/SNP Ref LD

Reference year

Adopted total

Sunite China (25) 2015

1000000

207 (16) 2014 1000000

Swiss Black-Brown Mountain Switzerland DAD-IS 2013 630 14500 9101 333 (11) 2012 14500

Swiss Mirror Switzerland DAD-IS 2013 314 1700 1607 262 (11) 2012 1700

Swiss White Alpine Switzerland DAD-IS 2013 1703 33000 26826 374 (11) 2012 33000

Tibetan China DAD-IS

903 (11) 2012 2300000

Valais Black Nose Switzerland DAD-IS 2013 593 16000 15116 288 (11) 2012 16000

Valais Red Switzerland DAD-IS 2013 143 1050 930 173 (11) 2012 1050

Valle del Belice Italy DAD-IS 2013 7964 202876

369 (13) 2012 202876

Wiltshire Australia DAD-IS 2012

6528 2720 100 (11) 2012 6528


Part (c) Reference list (sheep)

(1)Danchin-Burge,C., Palhiere,I., Francois,D., Bibe,B., Leroy,G. & Verrier,E. (2010) Pedigree analysis of seven small French sheep populations and implications for the management of rare breeds. Journal of Animal Science, 88, 505-516.

(2)Larroque, H., Barillet, F., Baloche, G., Astruc, J. M., Buisson, D., and et al. Toward genomic breeding programs in French dairy sheep and goats. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 2014. Vancouver.

(3)Kugler,W. (2009) Rare Breeds and Varieties of the Balkan Atlas 2009 Synonyms, Occurrence, Description of Rare Breeds in the Balkan Region http://www.save-foundation.net/pdf/BreedatlasBalkan.pdf. Monitoring Institute for Rare Breeds and Seeds in Europe / SAVE Foundation.

(4)Ghafouri-Kesbi,F., Eskandarinasab,M.P. & Hassanabadi,A. (2008) Investigation of genetic variability and inbreeding characteristics in a population of Zandi sheep. Canadian Journal of Animal Science, 88, 409-417.

(5)Pedrosa,V.B., Santana Junior,M.L., Oliveira,P.S., Eler,J.P. & Ferraz,J.B.S. (2010) Population structure and inbreeding effects on growth traits of Santa Inês sheep in Brazil. Small Ruminant Research , 93, 135-139.

(6) Leroy,G., Mary-Huard,T., Verrier,E., Danvy,S. & Charvolin,E. (2013) Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45.

(7)Maiwashe,A.N. & Blackburn,H.D. (2004) Genetic diversity in and conservation strategy considerations for Navajo Churro sheep. Journal of Animal Science, 82, 2900-2905.

(8)Li,M.H., Stranden,I. & Kantanen,J. (2009) Genetic diversity and pedigree analysis of the Finnsheep breed. Journal of Animal Science, 87, 1598-1605.


(10)Curkovic,M., Ramljak,J., Ivankovic,S., Mioc,B., Ivankovic,A., Pavic,V., Brka,M., Veit-Kensch,C.E. & Medugorac,I. (2015) The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection. Journal of Animal Breeding and Genetics, DOI: 10.1111/jbg.12160.

(11) Kijas,J.W., Lenstra,J.A., Hayes,B., Boitard,S., Porto Neto,L.R., San Cristobal,M., Servin,B., McCulloch,R., Whan,V., Gietzen,K., Paiva,S., Barendse,W., Ciani,E., Raadsma,H., McEwan,J., Dalrymple,B. & International Sheep Genomics Consortium (2012) Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10, e1001258.

(12)Al-Mamun,H.A., Clark,S.A., Kwan,P. & Gondro,C. (2015) Genome-wide linkage disequilibrium andgenetic diversity infive populations ofAustralian domestic sheep. Genetics Selection Evolution, 47.

(13)Mastrangelo,S., Di Gerlando,R., Tolone,M., Tortorici,L., Sardina,M.T., Portolano,B. & International Sheep Genomics Consortium (2014) Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds. BMC Genetics, 15.

(14)Garcia-Gamez,E., Sahana,G., Gutiérrez-Gil,B. & Arranz,J.J. (2012) Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genetics, 13.

(15)Baloche,G., Legarra,A., Salle,G., Larroque,H., Astruc,J.M., Robert-Granie,C. & Barillet,F. (2014) Assessment of accuracy of genomic prediction for French Lacaune dairy sheep. Journal of Dairy Science, 97, 1107-1116.

(16)Zhao,F. (2014) Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livestock Science, 170, 22-29.

(17)Chambers,F. (2006) Status of rare breeds of domestic farm livestock in Australia 2006 http://www.rbta.org/Pdf%20Files/RBTA%20%20Breeds%20Status%20Report%202006.pdf.


(18)Sahana,G., Gupta,S.C. & Nivsarkar,A.E. (2001) Garole: the proilific sheep of India. Animal Genetic Resources Information, 31, 55-63.

(19)Tawaf, R. Empowerment of small holder farmers business "Garut sheep" in west Java. International conference on sustainable agriculture and food security ; Challenges and Opportunities Universitas Padjadjaran Bandung 27-28 september 2011 (academia.edu) . 2011.

(20)Mokhtari,M.S., Miraei Ashtiani,S.R., Jafaroghli,M. & Gutiérrez,J.P. (2015) Studying Genetic Diversity in Moghani Sheep Using Pedigree Analysis. Journal of agricultiral science and technology, 17, 1151-1160.

(21)Kamalzadeh,A. & Aouladrabiei,M.R. (2009) Effects of Restricted Feeding on Intake, Digestion, Nitrogen Balance and Metabolizable Energy in Small and Large Body Sized Sheep Breeds. Asian-Australasian Journal of Animal Sciences, 22, 667-673.

(22)Yilmaz,O., Wilson,R.T., Kor,A., Cengiz,F. & Ertugrul,M. (2012) The farm animal genetic resources of Turkey: sheep – I – common and rare breeds. Bitlis Eren University Journal of Science and Technology, 2, 1-5.

(23)Huby, M., Griffon, L., Moureaux, S., de Rochambeau, H., Danchin-Burge, C., and Verrier, E. Genetic variability of six French meat sheep breeds in relation to their genetic management. Genetics Selection Evolution 35, pp. 637-655. 2003.

(24)GCSBA (2015) Gulf Coast Sheep Breeders Association http://gulfcoastsheep.info/about-the-breed/. Sandia, Texas, USA.

(25)Hui,Y. (2015) Mutton industry brings boom to local economy http://www.chinadaily.com.cn/opinion/2015-08/20/content_21659181.htm. China Daily, 20 August 2015.

(26)Pollott,G.E. (2016) The breeding structure of the British sheep industry 2012 http://www.eblex.org.uk/wp/wp-content/uploads/2014/09/The-breeding-structure-of-the-British-sheep-industry-2012-180914.pdf. EBLEX, Stoneleigh, Warwickshire.

(27)France Genetique Elevage (2015) Races ovines: Lacaune lait http://fr.france-genetique-elevage.org/Lacaune-lait.html.


(29) DEFRA (2013) UK country report on farm animal genetic resources 2012 https://www.gov.uk/government/publications/uk-country-report-on-farm-animal-genetic-resources-2012. Department of Environment, Food and Rural Affairs, London. DADIS


Supplementary Table S4: Horse references


(a) Breeds with 𝑵𝒆(𝐷𝐹)

Breed country source year brdg M brdg F hbk F "total" Adopted total

Ne by DF

Ref DF Ref year

Anglo-Arab France (17) 2013 116 1068 1184 83 (16) 2007

Arab France (17) 2013 711 2236 2947 (16) 2007

Ardennais France (17) 2013 185 1281 1466 151 (16) 2007

Auxois France (17) 2013 24 233 257 173 (16) 2007

Black-coated Asturcon pony

Spain DAD-IS 2011 758 1320 2319 2319 18.5 (13) 2008

Boulonnais France (17) 2013 41 358 399 59 (16) 2007

Brasileiro de Hipismo Brazil (1) 20000 206 (2) (3) 2011

Breton France (17) 2013 633 5171 5804 131 (16) 2007

Camarguais France (17) 2013 159 885 1044 46 (16) 2007

Cob normand France (17) 2013 41 375 416 97 (16) 2007

Comtois France (17) 2013 867 6928 7795 257 (16) 2007

Crioula Brazil (25) 2015 300000 300000 98.94 (28) 2010

Dole Norway DAD-IS 1994 27 284 311 311 152 (15) 1999

Franches-Montagnes Switzerland (18) 2008 21000 21000 91 (18) 2008

Friesian Netherlands DADIS 2004 49 20000 20000 20000 27 (5) 2000

Haflinger Italy (40) 2004 1122 8665 9787 9787 1250 (40) 2004

Hanoverian Germany DADIS 2006 522 19492 19492 20014 372 (11) 2000

Highland France (17) 2013 10 27 37 118 (16) 2007

Hispano-Arab Spain DADIS 2009 392 2852 2464 16 (4) 2004



Ne by DF

ref Ref year

Holstein Germany (21) 2010 225 7693 7918 55 (21) 2010

Hucul Slovakia DADIS 2009 119 250to500 375 48 (7) (8) 2007

Hucul Poland DAD-IS 2011 186 1415 2280 2280 32 (14) 2011

Icelandic horse Iceland DADIS 2009 1370 28948 28948 28948 113 (9) 2009

Konik (Polish Primitive) Poland DAD-IS 2011 156 973 1731 1731 37 (14) 2011

Landais France (17) 2013 25 65 90 33 (16) 2007

Lipizzan Slovakia DADIS 2009 13 105 140to180 160 117 (7) 2007

Lipizzan Europe (24) 2012 10766 10766 102 (26) 2001

Lusitano Portugal (22) 2009 5000 5000 28 (22) 2009

Merens France (17) 2013 75 484 559 (16) 2007

Nordland/Lyngen Norway DAD-IS 1994 27 154 181 181 42 (15) 1999

Norwegian Fjord Horse USA 207.8 (23) 2009

Pantaneiro Brazil (19) 2003 500 2600 3100 125 (20) 2009

Percheron France (17) 2013 179 1879 2058 191 (16) 2007

Poitevin France (17) 2013 33 163 196 156 (16) 2007

Pottock France (17) 2013 122 1170 1292 67 (16) 2007

Selle français France (17) 2013 467 9140 9607 134 (16) 2007

Shagya Arab Slovakia DADIS 2006 17

102 150to200 175 110 (7) 2007

Shetland France (17) 2013 384 1217 1601 132 (16) 2007

Slovak Sport Pony Slovakia DADIS 2006 7 60 60to120 90 81 (7) 2007

Sorraia Portugal DAD-IS 2014 143 146 420 420 11.6 (12) 2010

Spanish Anglo-Arab Spain DADIS 2009 3059 3388 3388 6447 62 (6) 2008



Ne by DF

ref Ref year

Spanish Anglo-Arab Spain DADIS 2009 3059 3388 3388 6447 65 (4) 2004

Spanish Arab Spain DADIS 2009 392 2852 2852 3244 38 (6) 2008

Spanish Purebred (Andalusian)

Spain DADIS 2009 34923 52558 168244 168244 51 (6)

2008

Spanish Purebred (Carthusian strain)

Spain 5600 22 (6)

2008

Spanish-Sport Horse (Caballo de Deporte)

Spain DADIS 2009 4101 5752 5752 9853 47 (4) 2004

Thoroughbred Hungary (24) 2015 37 185 224 159 (27) 2008

Trait du Nord France (17) 2013 13 197 210 189 (16) 2007

Trakehner Germany DADIS 2009 190 3363 3363 3553 157 (10) 2005

Trotteur français France (17) 2013 512 15580 16092 181 (16) 2007

Welsh Pony France (17) 2013 218 405 623 51 (16) 2007


(b) Breeds with 𝑵𝒆(𝐿𝐷)


M brdg F "total"

Adopted total

Ne by

LD/SNP Ref LD

Reference year

Akhal Teke US & Russia (29) 2013

3500 3500 302 (29) 2013

Andalusian US (29) 2013

185000 185000 329 (29) 2013

Arabian US (29) 2013

1000000 1000000 346 (29) 2013

Belgian US (29) 2015

50000 50000 431 (29) 2013

Caspian US (29) 2013

351 (29) 2013

Clydesdale US & UK (29) 2013

5000 5000 194 (29) 2013

Exmoor UK (29) 2013

2000 2000 216 (29) 2013

Fell_Pony UK (29) 2013

6000 6000 289 (29) 2013

Finnhorse Finland (29) 2013

19800 19800 575 (29) 2013

Florida Cracker US (35) 2015

1260 1260 171 (29) 2013

Franches-Montagnes Switzerland (29) 2013

21000 21000 316 (29) 2013

Franches-Montagnes Switzerland (18) 2008 21000 21000 62 (18) 2008

French Trotter France (17) 2013 512 15580

16092 233 (29) 2013

Hanoverian Germany (29) 2013

20000 20000 269 (29) 2013

Icelandic Sweden (29) 2013

180000 180000 555 (29) 2013

Jeju Korea (32) 2014

2000 2000 41 (32) 2013

Lusitano Portugal (29) 2013

12000 12000 391 (29) 2013

Mangalarga Paulista Brazil (36) 2014

31920 155 (29) 2013

Maremmano Italy (29) 2013

7000 7000 341 (29) 2013

Miniature US (29) 2013

185000 185000 521 (29) 2013

Mongolian Mongolia (29) 2013

2000000 2000000 751 (29) 2013

Morgan US (29) 2013

100000 100000 448 (29) 2013



M brdg F "total"

Adopted total

Ne by

LD/SNP Ref LD

Reference year

New Forest Pony UK (29) 2013

15000 15000 474 (29) 2013

North Swedish Horse Sweden (29) 2013

10000 10000 369 (29) 2013

Norwegian Fjord Norway DAD-IS 2013 33 203 236

335 (29) 2013

Paint USA (29) 2013

1000000 1000000 399 (29) 2013

Percheron USA (29) 2013

20000 20000 451 (29) 2013

Peruvian_Paso USA (29) 2013

25000 25000 433 (29) 2013

Puerto Rican Paso Fino Puerto Rico (29) 2013

250000 250000 321 (29) 2013

Quarter Horse USA (38) 2011

2640000 2640000 426 (29) 2013

Saddlebred USA (29) 2013

75000 75000 297 (29) 2013

Shetland Sweden (29) 2013 207 828 27000 27000 365 (29) 2013

Shire USA (29) 2013

7000 7000 357 (29) 2013

Standardbred global (29) 2013

290 (29) (29)

Standardbred Norway Norway (29) 2013

232 (29) 2013

Standardbred US USA (29) 2013

179 (29) 2013

Swiss_Warmblood Switzerland (29) 2013

15000 15000 271 (29) 2013

Tennessee Walking Horse USA (29) 2013

500000 500000 230 (29) (29)

Thoroughbred UK (30) 2015 181 8284

8465 100 (33) 2010

Thoroughbred Korea (31)

76 2006

2082 79 (34) 2014

Thoroughbred global (29) 2013

190 (29) 2013

Thoroughbred UK Ireland UK&Ireland (29) 2013

8465 8465 143 (29) 2013

Thoroughbred US US (37) 1993

250000 163 (29) 2013

Tuva Russia (29) 2013

30000 30000 533 (29) 2013


Part (c) Reference list (horses)

(1)ABCCH (2015) Historico BH http://brasileirodehipismo.com.br/site/nhtml/nstbh_historicobh.asp. Associação Brasileira de Criadores do Cavalo de Hipismo - ABCCH, Sao Paulo, Brazil.

(2)Medeiros,B.R., Bertoli,C.D., Garbade,P. & McManus,C.M. (2014) Brazilian Sport Horse: pedigree analysis of the Brasileiro de Hipismo breed. Italian Journal of Animal Science, 13, DOI: 10.4081/ijas.2014.3146.

(3)Dias, I. M. G. and Bergmann, J. A. G. Formation and population structure of the Brasileiro de Hipismo horse breed. Arquivo Brasileiro de Medicina Veterinaria e Zootecnia 52, pp. 647-654. 2000.

(4)Cervantes,I., Goyache,F., Molina,A., Valera,M. & Gutiérrez,J.P. (2009) Genealogical analyses in open populations: the case of three Arab derived Spanish horse breeds. Journal of Animal Breeding and Genetics, 126, 335-347.

(5)Sevinga,M., Vrijenhoek,T., Hesselink,J.W., Barkemas,H.W. & Groen,A.F. (2004) Effect of inbreeding on the incidence of retained placenta in Friesian horses. Journal of Animal Science, 82, 982-986.

(6)Cervantes,I., Goyache,F., Molina,A., Valera,M. & Gutiérrez,J.P. (2008) Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees. Journal of Animal Breeding and Genetics, 125, 301-310.

(7)Pjontek,J., Kadlecik,O., Kasarda,R. & Horny,M. (2012) Pedigree analysis in four Slovak endangered horse breeds. Czech Journal of Animal Science, 57, 54-64.

(8)Kusza,S., Priskin,K., Ivankovic,A., Jedrzejewska,B., Podgorski,T., Javor,A. & Mihok,S. (2013) Genetic characterisation and population bottleneck in the Hucul horse based on microsatellite and mitochondrial data. Biological Journal of the Linnaean Society, 109, 54-65.

(9)Hreidarsdottir,G.E., Arnason,T., Svansson,V. & Hallsson,J.H. (2014) Analysis of the history and population structure of the Icelandic horse using pedigree data and DNA analyses. Iceland Agricultural Science, 27, 63-79.

(10)Teegen,R., Edela,C. & Thaller,G. (2009) Population structure of the Trakehner horse breed. Animal, 3, 6-15.

(11)Hamann,H. & Distl,O. (2008) Genetic variability in Hanoverian warmblood horses using pedigree analysis. Journal of Animal Science, 86, 1503-1513.

(12)Kjollerstrom,H.J., Gama,L.T. & Oom,M.M. (2015) Impact of inbreeding on fitness-related traits in the highly threatened Sorraia horse breed. Livestock Science, in press.

(13)Goyache,F., Alvarez,I., Fernandez,I., Perez-Pardal,L., Royo,L.J. & Lorenzo,L. (2011) Usefulness of molecular based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcon pony. Journal of Animal Science, 89, 1251-1259.

(14)Mackowski,M., Mucha,S., Cholewinski,G. & Cieslak,J. (2015) Genetic diversity in Hucul and Polish primitive horse breeds. Archives Animal Breeding, 58, 23-31.

(15)Olsen,H.F., Klemetsdal,G., Ruane,J. & Helfjord,T. (2010) Pedigree structure and genetic variation in the two endangered Norwegian horse breeds: Døle and Nordland/Lyngen. Acta Agriculturae Scandinavica A, 60, 13-22.

(16)Leroy,G., Mary-Huard,T., Verrier,E., Danvy,S. & Charvolin,E. (2013) Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45.

(17)Haras nationaux (2015) Haras nationaux Equi-paedia http://www.haras-nationaux.fr/utilitaires/moteurs-de-recherche/equi-paedia.html. IFCE L'Institut français du cheval et de l'équitation.

(18)Hasler,H., Flury,C., Menet,S., Haase,H., Leeb,T., Simianer,H., Poncet,P.A. & Rieder,S. (2011) Genetic diversity in an indigenous horse breed - implications for mating strategies and the control of future inbreeding. Journal of Animal Breeding and Genetics, 128, 394-406.

(19)Santos,S.A., McManus,C., da Silva Mariante,A., Sereno,J.R.B., da Silva,J.A., Egito,A., Abreu,U.G.P., Comastri-Filho,J.A. & Lara,M.A. (2003) Estratégias de conservação in situ do cavalo


Pantaneiro http://www.cpap.embrapa.br/publicacoes/online/DOC55.pdf. Embrapa Pantanal, Corumba, MS.

(20)McManus,C., Santos,B.S.L., Dallago,S.R., Paiva,R.F.S., Martins,J., Braccini Neto,P.R., Marques,U.G.P. & Abreu,G.P. (2013) Evaluation of conservation program for the Pantaneiro horse in Brazil. Revista Brasileira de Zootecnia, 42, 404-413.

(21)Roos,L., Hinrichs,D., Nissen,T. & Krieter,J. (2015) Investigations into genetic variability in Holstein horse breed using pedigree data. Livestock Science, 177, 25-32.

(22)Vicente,A.A., Carolino,N. & Gama,L.T. (2012) Genetic diversity in the Lusitano horse breed assessed by pedigree analysis. Livestock Science, 148, 16-25.

(23)Bhatnagar,A.S., East,C.M. & Splan,R.K. (2011) Genetic variability of the Norwegian Fjord horse in north America. Animal Genetic Resources, 49, 43-49.

(24)LIF (2012) Lipizzan International Federation breeding history http://www.lipizzan-online.com/.

(25)ABCCC (2015) O cavalo crioulo http://cavalocrioulo.org.br/studbook/cavalo_crioulo.

(26) Zechner,P., Solkner,J., Bodo,I., Druml,T., Baumung,R., Achmann,E., Marti,F., Habe,E. & Brem,G. (2002) Analysis of diversity and population structure in the Lipizzan horse breed based on pedigree information. Livestock Production Science, 77, 137-146.

(27)Bokor,A., Jonas,D., Ducro,B., Nagy,I., Bokor,J. & Szabari,M. (2013) Pedigree analysis of the Hungarian Thoroughbred population. Livestock Science, 151, 1-10.

(28)Maciel,F.C., Bertoli,C.D., Braccini Neto,J., Cobuci,S.A., Paiva,C. & McManus,C. (2014) Population structure and genealogical analysis of the Brazilian Creole Horse. Animal Genetic Resources, 54, 115-125.

(29)Petersen,J.L. (2015) Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One, 8, e54997.

(30)EFTBA (2015) Thoroughbred Breeders' Association http://www.eftba.eu/member.php?id=18. European Federation of Thoroughbred Breeders' Associations http://www.eftba.eu/.

(31)Korean Racing Authority (2015) Mare returns 2014 Korean Stud Book http://studbook.kra.co.kr/eng/html/eng_breed_sts3.jsp?year=2014&x=25&y=7. Gwacheon-si, Gyeonggi-do, Korea.

(32)Do,K.-T., Lee,J.-H., Lee,H.-K., Kim,J. & Park,K.-D. (2014) Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse. Journal of Animal Science and Technology, 56.

(33)Corbin,L.J., Blott,S.C., Swinburne,J.E., Vaudin,M., Bishop,S.C. & Woolliams,J.A. (2010) Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics, 41, 8-15.

(34)Lee,Y.-S. (2014) Estimating effective population size of thoroughbred horses using linkage disequilibrium and theta (4 Nµ) value. Livestock Science, 168, 32-37.

(35)Levy,J. (2015) Personal communication Florida Cracker horses 11 Dec 2015.

(36)Pieragostini,E., Rizzi,R., Bramante,G., Rosati,A., Perrotta,G. & Caroli,A. (2015) Genetic study of Murgese horse from genealogical data and microsatellites. Italian Journal of Animal Science, 4, 197-202.

(37)Hall,S.J.G. (2005) The horse in human society. The domestic horse: the origins, development and management of its behaviour (eds D. S. Mills & S. M. McDonnell), pp. 23-32. Cambridge University Press, Cambridge.

(38)Petersen,J.L. (2013) The American Quarter Horse: population structure and relationship to the Thoroughbred. Journal of Heredity, 106.

(39) Hovermale,J. (2016) Personal communication 7 January 2016. Belgian Draft Horse Corporation, Wabash, IN, USA.


(40) Sabbioni,A., Beretti,V., Trezzi,M.F. & Superchi,P. (2007) Genetic variability and population structure in the Italian Haflinger horse from pedigree analysis. Ann.Fac.Medic.Vet.di Parma, 27, 199-210.


Supplementary Table S5: pig breeds



Breed country source year brdg M brdg F hbk F "total" Ne by DF Ref DF Reference

year Adopted

total

Alentejana Portugal DAD-IS 2013 363 5254

31398 26.76 (16) 2003-2010 31398

Angler Sattelschwein Germany DAD-IS 2010 15 58

73 73 (4) 2008 73

Belgian Landrace Belgium (3) 2004 62 797

859 88 (3) 2004 859

Berkshire USA DAD-IS 2007

44624 77 (2) 2007 44624

Berkshire UK (27) (28) 2012 36 48 680 716 47 (27) 2012 716

Black Slavonian Croatia (11) 2014 163 1064

1227 92 (11) 2014 1227

Blonde Mangalitsa Hungary DAD-IS 2011 142 3768

3910 58 (18) 2011 3910

British Landrace UK (27) (28) 2011 12 13 693 705 39 (27) 2010 705

Bunte Bentheimer Germany DAD-IS 2010 66 249

315 48 (4) 2008 315

Bunte Bentheimer Germany (9) 2003 24 95

119 24 (9) 2003 119

Cinta Senese Italy (8) 2007 252 1487

1739 267 (8) 2007 1739

Czech Landrace Czech Republic

76 (1) 2013

Czech Large White dam line Czech Republic DAD-IS 2013 345 4030 2327 7500 74 (1) 2013 7500

Czech Large White sire line Czech Republic DAD-IS 2013 210 300 272 2500 50 (1) 2013 2500

Duroc Czech Republic DAD-IS 2013

236 1100 35 (1) 2013 1100

Duroc USA DAD-IS 2007

83621 113 (2) 2007 83621

Duroc Canada (14) 2007-2008 40263

40263 72 (15) 2008 40263

Edelschwein Germany DAD-IS 2010 261 4972

5233 297 (4) 2008 5233



year Adopted

total

German Landrace Germany DAD-IS 2010 283 13091

13375 291 (4) 2008 13375

Guadyerbas Spain (6) 2000 14 42

56 23 (6) 1999 56

Hampshire USA DAD-IS 2007

45078 109 (2) 2007 45078

Hampshire Canada (13) 2007-2008 50

50 14 (15) 2008 50

Lacombe Canada (13) 2007-2008 2647

2647 36 (15) 2008 2647

Landrace USA DAD-IS 2007

34229 74 (2) 2007 34229

Landrace Austria DAD-IS 2002 255 3066

5000 415 (17) 2001 5000

Landrace Canada (13) 2007-2008 66140

66140 125 (15) 2008 66140

Large Black UK (27) (28) 2011 58 84 362 420 49 (27) 2010 420

Large White Austria DAD-IS 2002 457 5260

10000 181 (17) 2001 10000

Large White UK (27) (28) 2011 69 119 619 688 86 (27) 2009 688

Malhado de Alcobaça Portugal (7) 2004

160 160 25 (7) 2004 160

Middle White UK (27) (28) 2011 47 75 391 438 36 (27) 2011 438

Moura Brazil (12) 2014 10 20

30 30 (12) 2014 30

Piau Brazil (10) 2014 5 20

25 44 (10) 2011 25

Pietrain Czech Republic DAD-IS 2013 91

900 83 (1) 2013 900

Pietrain Germany DAD-IS 2010 2434 3365

5799 281 (4) 2008 5799

Pietrain Austria DAD-IS 2002 263 1154

5000 415 (17) 2001 5000

Pietrain Germany DAD-IS 2005 4710 4970

6680 315 (5) 2005 6680



year Adopted

total

Pietrain Belgium (3) 2004 605 1759

2364 125 (3) 2004 2364

Red Mangalitsa Hungary DAD-IS 2011 71 1525

1596 27.8 (18) 2011 1596

Rote Husumer Germany DAD-IS 2010 9 22

31 31 (4) 2008 31

Schwabisch Hallische Germany DAD-IS 2010 15 204

219 43 (4) 2008 219

Swallow-Bellied Mangalitsa Hungary DAD-IS 2011 55 1038

1093 55 (18) 2011 1093

Welsh UK (27) (28) 2011 75 157 793 868 38 (27) 2009 868

Yorkshire USA DAD-IS 2007

128093 113 (2) 2007 128093



Breed country source year brdg M brdg F hbk F "total" Ne by LD/SNP

Ref LD/SNP

Ref. year

Adopted total

Bisaro Portugal DAD-IS 2013 385 3737

28078 74 (24) 2013 28078

Chato Murciano Spain DAD-IS 2012 12 150

162 59 (24) 2013 162

Finnish Landrace Finland (19) 2009

2000

2000 80 (19) 2009 2000

Finnish Yorkshire Finland (19) 2009

2000

2000 55 (19) 2009 2000

Guadyerbas Spain (25) 2000 14 42

56 36 (25) 2014 56

Guinea USA (21) 2014

3178 431 (23) (26) 2015 3178

Korean Native Korea (20) 2003

68006 33 (20) 2014 68006

Landrace Korea DAD-IS

27 (20) 2014

Manchado de Jabugo Spain DAD-IS 2013 10 20

30 46 (24) 2013 30

Mulefoot USA (22) 2006

200 145 (23) (26) 2015 200

Negro Iberian Spain DAD-IS 2013 518 6035

31923 95 (24) 2013 31923

Ossabaw Island USA

191 (23) (26) 2015

Red Wattle USA (14) 2014 71 119

190 381 (23) (26) 2015 190

Retinto Spain DAD-IS 2013 1745 50391

112619 88 (24) 2013 112619

Saddleback USA

57 (23) (26) 2015

Tamworth USA

477 (23) (26) 2015


Part (c) Reference list (pigs)

(1)Krupa,E., Zakova,E. & Krupova,Z. (2015) Evaluation of inbreeding and genetic variability of five pig breeds in Czech Republic. Asian-Australasian Journal of Animal Sciences, 28, 25-36.

(2)Welsh,C.S., Stewart,T.S., Schwab,C. & Blackburn,H.D. (2010) Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation. Journal of Animal Science, 88, 1610-1618.

(3)Janssens, S., Depuydt, J., Serlet, S., and Vandepitte, W. Genetic variability in pigs assessed by pedigree analysis: the case of Belgian Landrace NN and Pietrain in Flanders. 56th Annual meeting of the European Association for Animal Production, June 4th - 8th, 2005, Uppsala Sweden, Commission on Animal Genetics, Session G2.39 . 2005.

(4)Tholen, E., Staack, J., Muller, P., and Ingwersen, J. Degree of endangerment of different German pig herdbook populations. 9th World Congress on Genetics Applied to Livestock Production. Leipzig August 1-6, 2010. http://www.kongressband.de/wcgalp2010/assets/pdf/0264.pdf . 2010.

(5)Habier, D., Götz, K.-U., and Dempfle, L. Breeding programme for Piétrain pigs in Bavaria with an estimation of genetic trends and effective population size. Livestock Science 123, pp. 187-192. 2009.

(6)Toro,M.A., Rodriganez,J., Silio,L. & Rodriguez,C. (2000) Genealogical analysis of a closed herd of black hairless Iberian pigs. Conservation Biology, 14, 1843-1851.

(7)da Gama,L.T., Carolino,N. & Vicente,A. (2008) Monitoring of livestock breeds at risk in Portugal. http://www.save-foundation.net/ELBARN/pdf/Gama_Livestock%20risks%20Portug.pdf.

(8)Crovetti, A., Bozzi, R, Nardi, L., Gallo, M., Buttazzoni, L., and Franci, O. Pedigree analysis of Cinta Senese breed. Proceedings of the 6th International Symposium on the Mediterranean Pig October 11 - 13, 2007 Messina - Capo d'Orlando (ME), Italy , pp. 35-40. 2007.

(9)Sundag,C.K.G., Wrede,J. & Distl,O. (2006) Analyse der Populationsstruktur des Bunten Bentheimer Schweins. Archiv fur Tierzucht, 49, 447-461.

(10)Veroneze,R., Lopes,P.S., Guimaraes,S.E.F., Guimaraes,J.D., Costa,E.V., Faria,V.R. & Costa,K.A. (2014) Using pedigree analysis to monitor the local Piau pig breed conservation program. Archivos de Zootecnia, 63, 45-54.

(11)Lukic,B., Smetko,A., Mahnet,Z., Klisanic,V., Spehar,M., Raguz,N. & Kusec,G. (2015) Population genetic structure of autochthonous Black Slavonian pig. Poljoprivreda, 21, 28-32.

(12)Carneiro,H., Paiva,S.R., Ledur,M., Figueiredo,E.A.P., Grings,V.H., Silva,F.C.P. & McManus,C. (2015) Pedigree and population viability analyses of a conservation herd of Moura pig. Animal Genetic Resources, 54, 127-134.

(13)CLRC (2015) Canadian Swine Breeders` Association Registrations 2014: http://www.clrc.ca/swinebybreed2014.pdf. Canadian Livestock Records Corporation, Ottawa.

(14)RWHA (2015) Red Wattle Hog Association www.redwattle.com.

(15)Melka,M.G. & Schenkel,F. (2010) Analysis of genetic diversity in four Canadian swine breeds using pedigree data. Canadian Journal of Animal Science, 90, 331-340.

(16)Borges,M.B. (2013) Caracterização demográfica da raça suína Alentejana. Universidade de Lisboa Faculdade de Medicina Veterinária.

(17)Baumung, R., Willam, A., Fischer, C., and Solkner, J. Pedigree analysis of pig breeds in Austria. Proceedings of the 7th World Congress on Genetics Applied to Livestock Production, Montpellier, France, August, 2002.Session 3 2002 pp.1-4 . 2002.

(18)Posta,J., Szabo,P. & Komlosi,I. (2015) Pedigree analysis of Mangalica pig breeds DOI: 10.1515/aoas-2015-0075. Annals of Animal Science.

(18)Toro,M.A., Rodriganez,J., Silio,L. & Rodriguez,C. (2000) Genealogical analysis of a closed herd of black hairless Iberian pigs. Conservation Biology, 14, 1843-1851.

(19)Uimari,P. & Tapio,M. (2011) Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. Journal of Animal Science, 89, 609-614.


(20)Park, J.-E. Estimation of linkage disequilibrium and effective population size using whole genome single nucleotide polymorphisms in Korean native pig and Landrace. 10th WCGALP . 2015.

(21)Bryan,M. (2014) American Guinea Hogs - Pedigree Analysis and Breeding Recommendations http://albc-usa.etapwss.com/images/uploads/docs/American_Guinea_Hogs_Recommendations.pdf. The Livestock Conservancy.

(22)ALBC (2006) Mulefoot hog https://www.livestockconservancy.org/index.php/heritage/internal/mulefoot American Livestock Breeds Conservancy, Pittsboro, NC, USA.

(23)Lamberson,W.R. (2015) Personal communication.

(24)Herrera-Viedma,E., Megens,H.-J., Groenen,M.A.M., Ramis,G., Bosse,M., Perez-Enciso,M. & Crooijmans,R.P.M.A. (2013) Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genetics, 14:106.

(25)Suarez, A. V., Woolliams, J. A., Tenesa, A., Fernandez, A., and Villanueva, B. Estimation of ancient and recent effective population size from linkage disequilibrium in a closed herd of Iberian pigs. Proceedings, 10th World Congress of Genetics Applied to Livestock Production . 2014.

(26) Roberts,K.S. & Lamberson,W.R. (2015) Relationships among and variation within rare breeds of swine. Journal of Animal Science, 93, 3810-3813.


(28) DEFRA (2013) UK country report on farm animal genetic resources 2012 https://www.gov.uk/government/publications/uk-country-report-on-farm-animal-genetic-resources-2012. Department of Environment, Food and Rural Affairs, London.

https://www.livestockconservancy.org/index.php/heritage/internal/mulefoot


Supplementary Table S6: goat breeds




Ne by DF Ref Ref year

Alpine France (05) 2012

125797 125797 143 (05) 2006-2009

Angora France (05) 2012

1271 1271 76 (06) 2009

Boer Brazil (07) (12) 2015

426.9 426.9 173.5 (07) 2012

Chevre des Fosses France (13) 2006 170 515

685 685 43.9 (03) 2005

Dutch Landrace Netherlands DAD-IS 2009 344 2131

2475 2475 192 (08) 2005

Icelandic Iceland DADIS 2009 70 585 585 700 700 5.1 (02) 2012

Payoya Spain (04) 2011

18.1 (04) 2011

Poitevine France (13) 2006 200 2600

2800 2800 77.5 (03) 2004

Provencale France (13) 2006 65 900

965 965 455 (03) 2005

Saanen France (05) 2012

183611 183611 120 (05) 2006-2009

White Shorthaired goat Slovakia DAD-IS 2013

774

7199 7199 182 (09) 2011


Breed country source year brdg M brdg F hbk F "total" Adopted

total

Ne by LD/SNP Ref Ref year

Alpine Canada (10) (12) 1999 1105 5746 5746 149 (01) 1995

Boer Canada (10) (12) 2009 1064 5533 5532.8 77 (01) 1995

Boer Australia

46 (01) 1995

Cashmere Australia

41 (01) 1995

La Mancha Canada (10) (12) 1999 264 1373 1372.8 62 (01) 1995

Nubian Canada (10) (12) 1999 826 4295 4295.2 61 (01) 1995

Rangeland Australia

104 (01) 1995

Saanen Canada (10) (12) 1999 483 2512 2511.6 113 (01) 1995

Toggenburg Canada (10) (12) 1999 363 1888 1887.6 38 (01) 1995


Part (c) Reference list (goats)

(1)Brito,L.F., Jafarikia,M., Grossi,D.A., Kijas,J.W., Porto-Neto,L.R., Ventura,R.V., Salgorzaei,M. & Schenkel,F.S. (2015) Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats. BMC Genetics, 16.

(2)Baldursdottir,B.K., Kristjansson,T. & Hallsson,J.H. (2012) Diversity of the Icelandic goat breed assessed using population data. Acta Agriculturae Scandinavica A, 62, 13.

(3)Danchin-Burge,C. (2006) What future can we foresee for rare French goat breeds ? Some predictions based on a genetic studyof three local breeds. http://www.journees3r.fr/IMG/pdf/2006_8_variabilite_genetique_10_Danchin-Bruge.pdf. Rencontres Recherches Ruminants, 13, 258.


(5)Larroque, H., Barillet, F., Baloche, G., Astruc, J. M., Buisson, D., and et al. Toward genomic breeding programs in French dairy sheep and goats. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. 2014. Vancouver.

(6)Danchin-Burge,C., Allain,D., Clement,V., Piacere,A., Martin,P. & Palhiere,I. (2012) Genetic variability and French breeding programs of three goat breeds under selection. Small Ruminant Research, 108, 36-44.

(7)Menezes,L.M., Sousa,W.H., Cavalcanti Filho,E.P., Cartaxo,F.Q., Viana,J.A. & Gama,L.T. (2015) Genetic variability in a nucleus herd of Boer goats in Brazil assessed by pedigree analysis. Small Ruminant Research, 131, 85-92.

(8)Mucha,S. & Windig,J.J. (2009) Effects of incomplete pedigree on genetic management of the Dutch Landrace goat. Journal of Animal Breeding and Genetics, 126, 250-256.

(9)Oravcova,M. (2013) Pedigree analysis in White Shorthaired goat: First results. Archiv fur Tierzucht, 56, 547-554.

(10)CLRC (2015) Purebred goats registered in 1999. http://www.clrc.ca/goatsreg1999.shtml. Canadian Livestock Records Corporation, Ottawa.

(11)CLRC (2015) Canadian Meat Goat Association registrations 2009 http://www.clrc.ca/associations/meatgoats/statistics/meatgoats2009.pdf. Canadian Livestock Records Corporation, Ottawa.

(12) Hall,S.J.G. (2011) Number of females in cattle, sheep, pig, goat and horse breeds predicted from a single year's registration data. Animal, 5:6, 980-985.

(13) Danchin-Burge, C. and Verrier, E. (2008) What future for the rare French goat breeds? Some answers thanks to a pedigree analysis on three breeds http://www.eaap.org/Previous_Annual_Meetings/2008Vilnius/Papers/published/08_Danchin-Burge.pdf. 59th EAAP meeting August 24-27 2008 Vilnius, Lithuania , pp. 1-6.

of 48 Hall, S.J.G. Effective population sizes in livestock

Supplementary Table S7 Variation among UK cattle breeds in values of the input variables for Hill’s equation

Breeds are classified according to the female/male ratio (F/M) in calf registrations during the year. (regs: registrations; dau: daughter; GL: generation length; s-m sire-son, s-f sire-daughter; d-m dam-son; d-f dam-daughter)

(a) Breeds with low F/M ratio

Breed

year

Tota

l sires

M c

alf r

egs

F c

alf r

egs

Ratio F

/M

calv

es

Ratio

dam

s/s

ire

Tota

l da

ms

Mean

sons/s

ire

Vari

ance

sons/s

ire

Mean

da

u. /

sire

Vari

ance

dau.

/ sire

covariance

sire

GL s

-m

GL s

-f

GL d

-m

GL d

-f

variance

son/d

am

variance

dau./

dam

covariance

dam

Whitebred Shorthorn

2011 28 48 49 1 3.2 90 1.71 4.8 1.75 3.6 1.852 5.7 5.8 6.1 6 1.456 0.146 -0.0297

Poll Hereford

2011 544 1747 2227 1.3 7.3 3974 3.2 14.45 4.12 18.2 9.644 4.1 8.2 41.668 2.486 -0.0187

Hereford 2011 302 957 1369 1.4 7.7 2326 3.18 12.65 4.53 17.8 9.767 5.3 5.6 17.739 0.822 -0.0144 Aberdeen Angus (orig.)

2011 16 20 37 1.9 3.6 57 1.19 2.3 2.38 8.25 1.592 5.5 7.2 1.226 0.096 -0.0331

Beef Shorthorn

2008 370 956 1784 1.9 7.4 2740 2.58 12.86 4.82 25.5 9.947 5.1 5.4 31.37 1.301 -0.0176

Hereford (trad.)

2011 60 155 301 1.9 7.6 456 2.58 18.76 5.02 26.2 13.35 8.7 9.1 3.005 0.069 -0.0099

Irish Moiled 2011 68 33 136 4.1 2.4 157 0.5 0.75 2.06 4.19 0.631 5.3 5.2 5.4 5.4 9.344 0.856 -0.0687

Shetland 2011 63 33 147 4.5 2.9 180 0.52 0.74 2.33 4.68 0.449 7.003 0.5 -0.0476 British White

2011 100 70 343 4.9 4.0 398 0.7 1.34 3.43 6.89 0.292 5 5.2 5.6 5.4 14.85 0.866 -0.0433

Mean for F/M <5

7.627 3.38 12.8 5.28 Mean generation length 5.91 years

14.19 0.793 -0.0315


(b) Breeds with medium F/M ratio

Breed

year

Tota

l sires

M c

alf r

egs

F c

alf r

egs

Ratio F

/M

calv

es

Ratio

dam

s/s

ire

Tota

l da

ms

Mean

sons/s

ire

Vari

ance

sons/s

ire

Mean

da

u. /

sire

Vari

ance

dau.

/ sire

covariance

sire

GL s

-m

GL s

-f

GL d

-m

GL d

-f

variance

son/d

am

variance

dau./

dam

covariance

dam

Dairy Shorthorn

2008 136 87 684 7.9 5.7 2405 0.64 2.08 5.02 69.1 2.371 14.7 7.8 1.10 0.022 -0.0002

Gloucester 2011 32 8 66 8.3 2.2 70 0.25 0.26 2.07 4.83 -0.48 5.7 5.2 6 5.3 5.27 0.473 -0.0798

British Friesian

2011-

2012 182 236 2352 9.96 15 2820 0.81 3.52 10.3 313 21.45 10.2 8

12.7 0.098 -0.0054 Lincoln Red

2011 155 74 771 10.4 5.2 810 0.4 1.04 4.97 18.8 0.961 5.4 4.9 5.3 5.1 28.1 1.129 -0.0364

Luing 2011 227 168 1795 10.7 8.5 1894 0.75 3.72 8.01 31.9 1.344 4.0 4.6 5.7 5.5 41.1 1.046 -0.0229 South Devon

2011 527 223 3099 13.9 6.3 3322 0.42 1.408 5.88 20.7 0.794 6.1 6 76.4 2.166 -0.0247

Dexter 2008 545 120 2215 18.5 4.3 2335 0.22 0.32 4.06 13.7 1.728 6.5 6.7 75.5 2.856 0.0341 Lincoln Red (orig.)

2008 33 9 171 19 5.5 180 0.27 0.33 5.18 20.2 -0.2 6.8 5.9 8.12 0.428 -0.0480

Red Poll 2011 159 46 901 19.6 5.6 868 0.31 0.052 5.97 35.2 -0.21 9.4 6 6.5 5.3 18.1 0.322 -0.0200

Mean for F/M 5-20


29.6 0.949 -0.0226


(c) Breeds with high F/M ratio

Breed year

Tota

l sires

M c

alf r

egs

F c

alf r

egs

Ratio F

/M

calv

es

Ratio

dam

s/s

ire

Tota

l da

ms

Mean

sons/s

ire

Vari

ance

sons/s

ire

Mean

da

u. /

sire

Vari

ance

dau.

/ sire

covariance

sire

GL s

-m

GL s

-f

GL d

-m

GL d

-f

variance

son/d

am

variance

dau./

dam

covariance

dam

Longhorn 2009 309 72 1606 22.3 5.4 1613 0.23 0.38 5.2 23.4 0.204 5.92 5.6 5.9 5.6 54.71 1.88 -0.034 Welsh Black

2010 345 90 2041 22.7 6.2 2131 0.26 0.54 5.92 24.5 1.121 6.1 6.3 44.68 1.066 -0.022

Dairy Shorthorn grading

2008 146 51 1179 23.1 9.1 1325 0.3 0.71 6.97 82.3 1.769 6.7 6.7 17.25 0.318 -0.015

Ayrshire 2011 405 123 2930 23.8 7.5 3053 0.31 1.18 7.23 138 4.645 62.17 1.432 -0.021

Highland 2009 358 53 1708 32.2 4.9 1793 0.18 0.43 4.82 19.3 0.423 5.7 6.8 54.14 1.89 -0.032

Guernsey 2011 99 28 943 33.7 9.8 971 0.29 0.41 9.56 163 3.477 5.6 6.4 22.91 0.59 -0.024

Mean for F/M >20


42.64 1.196 -0.025


Supplementary Table S8 Ratios of effective to census population sizes (𝑵𝒆/𝑵𝒄) 𝒊n descending order of median. Species classified according to the technique employed

Species and

technique median mean variance CV % max min n

Pigs LD 0.0878 0.457 0.4134 140.8 2.01 0.00049 12

Pigs DF 0.0553 0.199 0.1377 186.6 1.75 0.00085 43

Goats DF 0.0437 0.114 0.0272 144.6 0.47 0.00065 10

Horse DF 0.0366 0.243 0.2882 220.8 3.19 0.00030 42

Goats LD 0.0230 0.027 0.0002 48.0 0.05 0.01392 6

Sheep DF 0.0166 0.059 0.0090 160.0 0.49 7.86E-05 84

Sheep LD 0.0151 0.130 0.0829 221.7 1.43 4.09E-06 56

Horse LD 0.0150 0.024 0.0009 124.8 0.14 0.00016 37

Cattle DF 0.0104 0.050 0.0215 292.8 1.27 2.4E-05 124

Cattle LD 0.0004 0.020 0.0075 436.0 0.55 8.6E-07 53


Supplementary Figure S1

Caption to Supplementary Figure S1

Cattle: scattergram from Table 3, with regression line and confidence limits (P <

0.05). y-axis: 𝑵𝒆(𝛥𝐹); x-axis: log10𝑵𝒆(Wright)




Cattle: scattergram from Table 3, with regression line and confidence limits (P <

0.05). y-axis: 𝑵𝒆(𝐿𝐷); x-axis: log10𝑵𝒄




Sheep: scattergram from Table 3, with regression line and confidence limits (P <





Horses: scattergram from Table 3, with regression line and confidence limits (P <





Pigs: scattergram from Table 3, with regression line and confidence limits (P < 0.05).

y-axis: 𝑵𝒆(𝐿𝐷); x-axis: log10𝑵𝒆(Wright)

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